Identification of suitable reference genes for expression studies in pomegranate under different biotic and abiotic stress conditions

Doddaraju, Pushpa; Dashyal, Mahesh S.; Kumar, Pavan

doi:10.1007/s11033-021-06389-8

Cited by 6 publications

(4 citation statements)

References 43 publications

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“…It was also found that GAPDH maintained stable expression in different organs and at different stages of fruit development in strawberry [25]. Both GAPDH and CYP maintained good stability in pomegranate when subjected to biotic and abiotic stresses [26]. The most consistently expressed reference genes in blueberry were UBC9 and GAPDH when attacked by Monilinia vaccinii-corymbosi [27].…”

Section: Discussionmentioning

confidence: 86%

Identification of Suitable Reference Genes for qRT-PCR Normalization in Kiwifruit

et al. 2022

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Reference genes are used for the correction of qRT-PCR data, and it is necessary to investigate the optimum reference gene under certain conditions. The expression levels of seven traditional reference genes ACT1, ACT2, GAPDH, 18S rRNA, UBQ, TUB and CYP were analyzed using qRT-PCR in different varieties, tissues, developmental stages and hormone (or pollen polysaccharide) treatments in kiwifruit. Gene expression stability was assessed with the help of three common software (geNorm, NormFinder, BestKeeper), and the minimum number of reference genes necessary for normalization was also determined. GAPDH, ACT1 and ACT2 were selected as reference genes for different genotypes of kiwifruit. GAPDH and UBQ were the best combinations of reference genes for root, stem, leaf, flower and fruit. GAPDH and ACT1 could be the preferred reference genes for normalization of qRT-PCR data during fruit development. The pairing of ACT1 and UBQ constituted the optimal combination of reference genes in kiwifruit treated with different hormones (or pollen polysaccharide). This study provides a new and reliable option for the use of reference genes in the analysis of gene expression patterns of interest in kiwifruit.

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Section: Discussionmentioning

confidence: 86%

Identification of Suitable Reference Genes for qRT-PCR Normalization in Kiwifruit

et al. 2022

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“…As a result, hundreds of transcriptome profiling studies have been carried out to date, proving that RNA-seq is an advanced method to decipher the molecular mechanism underlying these interactions [ 11 ]. Simultaneously, these approaches would aid in the continuous identification of new resistance genes, which is crucial in setting the stage for upcoming breeding programs and improving resistance to biotic stresses [ 12 , 13 ]. For instance, 186 R2R3-MYB transcription factors (TFs), identified from pomegranate genome, are involved in regulating plant development, metabolite accumulation, and defense responses; similar occurs for U-box gene family entailed in abiotic stresses [ 14 , 15 ].…”

Section: Introductionmentioning

confidence: 99%

Deciphering the Interaction between Coniella granati and Pomegranate Fruit Employing Transcriptomics

Tsafouros,

Tsalgatidou,

Boutsika

et al. 2024

Life

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Pomegranate fruit dry rot is caused by Coniella granati, also referred as Pilidiella granati. In order to decipher the induced responses of mature pomegranates inoculated with the pathogen, an RNA-seq analysis was employed. A high number of differentially expressed genes (DEGs) were observed through a three-time series inoculation period. The transcriptional reprogramming was time-dependent, whereas the majority of DEGs were suppressed and the expression patterns of specific genes may facilitate the pathogen colonization at 1 day after inoculation (dai). In contrast, at 2 dai and mainly thereafter at 3 dai, defense responses were partially triggered in delay. Particularly, DEGs were mainly upregulated at the latest time point. Among them, specific DEGs involved in cell wall modification and degradation processes, pathogen recognition and signaling transduction cascades, activation of specific defense and metabolite biosynthesis-related genes, as well in induction of particular families of transcriptional factors, may constitute crucial components of a defense recruiting strategy employed by pomegranate fruit upon C. granati challenge. Overall, our findings provide novel insights to the compatible interaction of pomegranates—C. granati and lay the foundations for establishing integrated pest management (IPM) strategies involving advanced approaches, such as gene editing or molecular breeding programs for disease resistance, according to European Union (EU) goals.

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“…In addition, the cultivation of pomegranate provides a source of livelihood to over 2.5 lakh families in India (NRCP Annual Report, 2020). Although persistent efforts are being made in India to improve, promote and market the crop, various factors such as abiotic and biotic stressors, physiological limitations, genetic constraints, excessive growth rate, nutrient unavailability, as well as pest and disease infestations, have been identified as severe impediments to its growth 4 , 5 . Diseases such as wilt complex 6 , anthracnose 7 , bacterial blight 8 , Coniella fruit rot 9 , 10 , foliar diseases such as leaf spot and fruit spot disease 11 are some of the major diseases that affect the pomegranate crop.…”

Section: Introductionmentioning

confidence: 99%

Improved species level bacterial characterization from rhizosphere soil of wilt infected Punica granatum

Das,

Sarangi,

Ravinath

et al. 2023

Sci Rep

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Pomegranate crops are prone to wilt complex disease, which is known to severely hamper the crop yield. There have been limited studies that have explored bacteria–plant–host associations in wilt complex disease affecting pomegranate crops. In the present study, wilt infected rhizosphere soil samples (ISI, ASI) in pomegranate were studied in comparison to a healthy control (HSC). The 16S metagenomics sequencing approach using the MinION platform was employed for screening of bacterial communities and predictive functional pathways. Altered physicochemical properties in the soil samples were recorded showing a comparatively acidic pH in the ISI (6.35) and ASI (6.63) soil samples to the HSC soil (7.66), along with higher electrical conductivity in the ISI (139.5 µS/cm), ASI soil (180 µS/cm), HSC soil sample (123.33 µS/cm). While concentration of micronutrients such as Cl and B were significantly higher in the ISI and ASI soil as compared to the HSC, Cu and Zn were significantly higher in the ASI soil. The effectiveness and accuracy of 16S metagenomics studies in identifying beneficial and pathogenic bacterial communities in multi-pathogen–host systems depend on the completeness and consistency of the available 16S rRNA sequence repositories. Enhancing these repositories could significantly improve the exploratory potential of such studies. Thus, multiple 16S rRNA data repositories (RDP, GTDB, EzBioCloud, SILVA, and GreenGenes) were benchmarked, and the findings indicated that SILVA yields the most reliable matches. Consequently, SILVA was chosen for further analysis at the species level. Relative abundance estimates of bacterial species showed variations of growth promoting bacteria, namely, Staphylococcus epidermidis, Bacillus subtilis, Bacillus megatarium, Pseudomonas aeruginosa, Pseudomonas putida, Pseudomonas stutzeri and Micrococcus luteus. Functional profiling predictions employing PICRUSt2 revealed a number of enriched pathways such as transporter protein families involved in signalling and cellular processes, iron complex transport system substrate binding protein, peptidoglycan biosynthesis II (staphylococci) and TCA cycle VII (acetate-producers). In line with past reports, results suggest that an acidic pH along with the bioavailability of micronutrients such as Fe and Mn could be facilitating the prevalence and virulence of Fusarium oxysporum, a known causative pathogen, against the host and beneficial bacterial communities. This study identifies bacterial communities taking into account the physicochemical and other abiotic soil parameters in wilt-affected pomegranate crops. The insights obtained could be instrumental in developing effective management strategies to enhance crop yield and mitigate the impact of wilt complex disease on pomegranate crops.

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Identification of suitable reference genes for expression studies in pomegranate under different biotic and abiotic stress conditions

Cited by 6 publications

References 43 publications

Identification of Suitable Reference Genes for qRT-PCR Normalization in Kiwifruit

Identification of Suitable Reference Genes for qRT-PCR Normalization in Kiwifruit

Deciphering the Interaction between Coniella granati and Pomegranate Fruit Employing Transcriptomics

Improved species level bacterial characterization from rhizosphere soil of wilt infected Punica granatum

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